Primary drive will not boot... partition problem

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I did a major oopsie with my PC. I'm running two hard drives - a master IDE drive (my old 60GB) and a newer SATA drive (200GB). I believe these two were set up incorrectly (when I was running my old XP the primary drive was E:/Windows etc)

Now I've upgraded to Vista and it set the 200GB to C:, which is what I wanted. However there were still files on the E: (60GB) drive. Still with me? I noticed that even though Windows said the now SLAVE 60GB drive was blank, I could not format it within Vista. So I used a disk formatting program to wipe it - a dumb idea.

Everything was fine, but when I boot up now it says DISK ERROR - god knows what I did but I think I messed up the partition - why would Vista be storing partition files on a slave drive anyway?

What I think I am going to have to do is install the OS on the 60GB drive, copy all my crap onto it and blank the 200GB and install vista on it again. I need to sort out my jumpers on the Hard disks as well - this problem was caused partly by my ignorance of running SATA and IDE side by side. On the other hand if I can fix the boot partition then my C: should boot vista again - all the files are there so what's the problem??

Worth noting is that even though I had deleted all the files on the 60GB drive when I was running vista on the 200GB (a brighter time for me) - it still would come up with the dual boot screen before starting up into Vista.

Any advice?

*** On further reading, I'm under the impression that if I booted with the XP CD, logged into the recovery console and ran bootcfg /rebuild, it will rebuild the boot.ini and my system might start again?
 
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